+Open data
-Basic information
Entry | Database: PDB / ID: 2fqx | ||||||
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Title | PnrA from Treponema pallidum complexed with guanosine | ||||||
Components | Membrane lipoprotein tmpC | ||||||
Keywords | TRANSPORT PROTEIN / ABC transport system / ligand-binding protein / guanosine / TmpC / tp0319 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Treponema pallidum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Brautigam, C.A. / Deka, R.K. / Tomchick, D.R. / Machius, M. / Norgard, M.V. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: The PnrA (Tp0319; TmpC) lipoprotein represents a new family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC)-like operon in Treponema pallidum Authors: Deka, R.K. / Brautigam, C.A. / Yang, X.F. / Blevins, J.S. / Machius, M. / Tomchick, D.R. / Norgard, M.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fqx.cif.gz | 79.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fqx.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 2fqx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/2fqx ftp://data.pdbj.org/pub/pdb/validation_reports/fq/2fqx | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34058.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Treponema pallidum (bacteria) / Gene: tmpC / Plasmid: pProEX HTa / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P29724 |
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#2: Chemical | ChemComp-GMP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.2 M ammonium acetate, 0.1 M sodium acetate, 30% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2005 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→36.9 Å / Num. all: 29393 / Num. obs: 29393 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 3 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PnrA as purified from E. coli Resolution: 1.7→36.9 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1499151.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.6248 Å2 / ksol: 0.335648 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→36.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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